The new site lacks dedicated pages pertaining to climate change, LGBT issues, education and more:

WhiteHouse.gov

Changes in links and file structure aren't a surprise. What happened on the server was that the Obama Administration's files were archived and replaced with those constructed in advance by the Trump Transition Team.

There does seem to still be a link between the new WhiteHouse.gov and Obama's archive. Some URLs left over from Obama's version of the site, like his page on the Iran Deal, redirect to the Obama Administration's new web home, while others, such as those pictured above, do not.